Hi,
running BWA mem (- PE; - Illumina), I'm getting the following error (replaced the ids):
[mem_sam_pe] paired reads have different names: "XXX:5:YYY:1:11102:4257:13510", "XXX:5:YYY:1:11102:15792:1058"
I checked the fastq file and found out that each read name is duplicated 7 times in the file (exact same name). However, the order of the read names is not matching between the pairs (see bold positions).
Example:
> grep -n "XXX:5:YYY:1:11102:4257:13510" R1.fastq
761397:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
862085:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
962773:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1063461:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1164149:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1264837:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1365525:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
> grep "XXX:5:YYY:1:11102:4257:13510" R2.fastq
761397:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
862085:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1028309:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1063461:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1229685:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1264837:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1365525:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
Is it ok for a fastq file to have multiple reads with the same read name?
If not, could this be a problem of BCL conversion?
How can I fix it?
Thanks for your help,
Stephan
PS: bwa mem command:
bwa mem -t 40 -v 1 hg19.fa R1.fastq R2.fastq > aln.sam
running BWA mem (- PE; - Illumina), I'm getting the following error (replaced the ids):
[mem_sam_pe] paired reads have different names: "XXX:5:YYY:1:11102:4257:13510", "XXX:5:YYY:1:11102:15792:1058"
I checked the fastq file and found out that each read name is duplicated 7 times in the file (exact same name). However, the order of the read names is not matching between the pairs (see bold positions).
Example:
> grep -n "XXX:5:YYY:1:11102:4257:13510" R1.fastq
761397:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
862085:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
962773:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1063461:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1164149:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1264837:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
1365525:@XXX:5:YYY:1:11102:4257:13510 1:N:0:AGGCAGAA+GCGATCTA
> grep "XXX:5:YYY:1:11102:4257:13510" R2.fastq
761397:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
862085:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1028309:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1063461:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1229685:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1264837:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
1365525:@XXX:5:YYY:1:11102:4257:13510 2:N:0:AGGCAGAA+GCGATCTA
Is it ok for a fastq file to have multiple reads with the same read name?
If not, could this be a problem of BCL conversion?
How can I fix it?
Thanks for your help,
Stephan
PS: bwa mem command:
bwa mem -t 40 -v 1 hg19.fa R1.fastq R2.fastq > aln.sam
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